I kid you not I just found out the damn cause...
I downloaded random OGG sample files to test to see if there's something about my OGG files that specifically the latest WACUP PB is picky about...
Get any OGG file, set the file attribute to 'Read-only' and then try playing it - WACUP cannot read the OGG file anymore, it cannot even display its metadata properly, if at all. In 'Read-only' for WACUP the 'file is corrupted' and its playback is skipped.
My MP3s, FLACs and MIDis are unaffected by 'Read-only' bug.
That leaves the window glitching issue which is also new in latest PB.
To test this, you need some application running that shows on the desktop, like Stickies (by Zhorn Software, freeware btw) or a windowed full screen app.
Minimize WACUP to tray. Then click on its tray icon to make it come up. You'll notice that in case of a running windowed full screen app WACUP's window doesn't show and in case of Stickies it hides behind the sticky note on the desktop, as if following 'bottom-most' order instruction. Even if to toggle WACUP to be 'Always On Top' it will have hard time following that instruction.
The previous PB didn't have issues showing its window, I also never had to enable 'Always On Top'.
The latest PB also has difficulties rendering the Drone skin by R. Peter Clark and 883DESIGN (year 2006 skin) - e.g.: playlist border disappears after going over an element which shows a 'tooltip'. The Drone skin tooltips now also have extra black bits which aren't supposed to exist.
Alright now, happy solving! Will be waiting for next PB.